Signatures of discriminative copy number aberrations in 31 cancer subtypes

B Gao, M Baudis - Frontiers in genetics, 2021 - frontiersin.org
Copy number aberrations (CNA) are one of the most important classes of genomic mutations
related to oncogenetic effects. In the past three decades, a vast amount of CNA data has …

From CFTR to a CF signalling network: a systems biology approach to study Cystic Fibrosis

M Najm, L Martignetti, M Cornet, M Kelly-Aubert… - BMC genomics, 2024 - Springer
Abstract Background Cystic Fibrosis (CF) is a monogenic disease caused by mutations in
the gene coding the Cystic Fibrosis Transmembrane Regulator (CFTR) protein, but its …

Identification of phenotype-specific networks from paired gene expression–cell shape imaging data

CG Barker, E Petsalaki, G Giudice, J Sero… - Genome …, 2022 - genome.cshlp.org
The morphology of breast cancer cells is often used as an indicator of tumor severity and
prognosis. Additionally, morphology can be used to identify more fine-grained, molecular …

Modeling in systems biology: Causal understanding before prediction?

S Barsi, B Szalai - Patterns, 2021 - cell.com
Modeling in systems biology: Causal understanding before prediction?: Patterns Skip to Main
Content Advertisement Patterns All content is freely available to readers and supported …

SiRCle (Signature Regulatory Clustering) model integration reveals mechanisms of phenotype regulation in renal cancer

A Mora, C Schmidt, B Balderson, C Frezza, M Bodén - bioRxiv, 2022 - biorxiv.org
Clear cell renal cell carcinoma (ccRCC) tumours develop and progress via complex
remodelling of the kidney epigenome, transcriptome, proteome, and metabolome. Given the …

Modeling causal signal propagation in multi-omic factor space with COSMOS

A Dugourd, P Lafrenz, D Mañanes, V Paton… - bioRxiv, 2024 - biorxiv.org
Understanding complex diseases requires approaches that jointly analyze omic data across
multiple biological layers, including signaling, gene regulation, and metabolism. Existing …

Convergent Transcriptomic Evidence Reveals the Dysfunctional Quantitative Mechanism of Synaptic Plasticity Control in ASD

C Kong, ZT Bing, L Yang, ZG Huang, WX Wang - bioRxiv, 2023 - biorxiv.org
A prominent endophenotype in Autism Spectrum Disorder (ASD) is synaptic plasticity
dysfunction, yet the molecular mechanism remains elusive. As a prototype, we investigated …

Differential Activity of MAPK signalling Defines Fibroblast Subtypes in Pancreatic Cancer

L Veghini, D Pasini, P Delfino, R Fang, D Filippini… - bioRxiv, 2023 - biorxiv.org
Fibroblast heterogeneity is increasingly recognised across cancer conditions. Given their
important contribution to disease progression, mapping out fibroblasts' heterogeneity is …

Application of perturbation gene expression profiles in drug discovery—From mechanism of action to quantitative modelling

B Szalai, DV Veres - Frontiers in Systems Biology, 2023 - frontiersin.org
High dimensional characterization of drug targets, compound effects and disease
phenotypes are crucial for increased efficiency of drug discovery. High-throughput gene …

Dynamic multi-omics and mechanistic modeling of kidney fibrosis progression

N Tüchler - 2024 - archiv.ub.uni-heidelberg.de
Chronic kidney disease (CKD) affects more than 10% of the world's population and causes
millions of deaths annually. Organ fibrosis is the main driver of the pathology underlying …